MD Topology | NMR | X-Ray

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Processing Information

QM Processing Stage

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Processing Stage Template Semi-Empirical QM (QM0) DFT QM (QM1) DFT Hessian QM (QM2)
Calculation None Energy Minization Energy Minization Hessian
Level of Theory None Semi-Empirical / SCF DFT (B3LYP/6-31G*) DFT (B3LYP/6-31G*)
Default Size Limit (Atoms) 1000 500 50 40
Content of MD Topology
Charges Derived From None MOPAC Merz-Singh-Kollman Merz-Singh-Kollman
Geometry  User Provided Optimized Optimized Optimized
Non-Bonded Interactions Bonds Rule Based:

Parameters are asigned from existing parameters with a set of rules based on atom types and geometry.

Hessian Based:

Force constant are calculated from the QM potential. New parameters are created when no suitable parameters exists.

Angles
Dihedrals

Data

Current Processing StateCompleted
Total Processing TimeNA (hh:mm:ss)

Molecule Information

Molecule Typeamino acid building block
Residue Name (RNME)F23
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms25
Net Charge0
Forcefieldmultiple
Molecule ID17302
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

GROMOS11 Files

Topology Files Structure Files
GROMOS11 United-Atom MTB
United-Atom PDB (optimised geometry)

Topology Information

Force Field Version54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date2014-02-03 13:07:16
Literature ReferenceDrazen Petrov, Christian Margreitter, Melanie Grandits, Chris Oostenbrink, Bojan Zagrovic; A Systematic Framework for Molecular Dynamics Simulations of Protein Post-Translational Modifications; PLOS Computational Biology, 2013, 9 (7), e1003154

Topology History

Other conformers for this molecule (1-100 of 632)

Compare All Topologies (633)RMSD Matrix (633)

Molid  Formula  Iupac  Atoms  Charge  Curation  Details  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17260 None - 15 -1 Manual N/A Compare with
17499 None - 25 0 Manual N/A Compare with
5011 None - 40 -4 Manual* N/A Compare with
1601 None - 17 0 Manual* N/A Compare with
17352 None - 15 0 Manual N/A Compare with
17145 None - 33 1 Manual N/A Compare with
17384 None - 23 0 Manual N/A Compare with
17236 None - 26 0 Manual N/A Compare with
17475 None - 23 0 Manual N/A Compare with
1567 None - 119 0 Manual* N/A Compare with
17268 None - 19 0 Manual N/A Compare with
17507 None - 29 0 Manual N/A Compare with
5795 None - 18 -1 Manual* N/A Compare with
1642 None - 18 0 Manual* N/A Compare with
17360 None - 30 0 Manual N/A Compare with
17153 None - 17 0 Manual N/A Compare with
17392 None - 18 0 Manual N/A Compare with
1525 None - 147 0 Manual* N/A Compare with
17244 None - 26 -1 Manual N/A Compare with
17483 None - 15 0 Manual N/A Compare with
1579 None - 143 0 Manual* N/A Compare with
17336 None - 30 1 Manual N/A Compare with
17276 None - 24 -1 Manual N/A Compare with
6451 None - 27 0 Manual N/A Compare with
17368 None - 29 0 Manual N/A Compare with
17220 None - 31 1 Manual N/A Compare with
17459 None - 28 0 Manual N/A Compare with
1550 None - 24 0 Manual* N/A Compare with
17252 None - 23 -2 Manual N/A Compare with
17491 None - 22 0 Manual N/A Compare with
4581 None - 161 -8 Manual* N/A Compare with
1589 None - 131 0 Manual* N/A Compare with
17344 None - 23 -2 Manual N/A Compare with
7282 None - 113 0 Manual* N/A Compare with
17376 None - 30 -1 Manual N/A Compare with
17228 None - 20 0 Manual N/A Compare with
17467 None - 31 0 Manual N/A Compare with
1558 None - 137 0 Manual* N/A Compare with
17201 None - 33 1 Manual N/A Compare with
17440 None - 25 0 Manual N/A Compare with
583 None - 15 0 Manual* N/A Compare with
1679 None - 31 0 Manual* N/A Compare with
17292 None - 28 0 Manual N/A Compare with
17531 None - 18 0 Manual N/A Compare with
3486 None - 9 0 Manual* N/A Compare with
17325 None - 25 0 Manual N/A Compare with
17177 None - 20 -1 Manual N/A Compare with
17416 None - 24 1 Manual N/A Compare with
212 None - 17 0 Manual* N/A Compare with
17209 None - 27 -2 Manual N/A Compare with
17448 None - 28 0 Manual N/A Compare with
1510 None - 161 0 Manual* N/A Compare with
2002 None - 24 0 Manual* N/A Compare with
17300 None - 18 0 Manual N/A Compare with
17539 None - 19 -2 Manual N/A Compare with
3505 None - 18 0 Manual* N/A Compare with
17333 None - 30 1 Manual N/A Compare with
163 None - 13 0 Manual* N/A Compare with
17185 None - 15 0 Manual N/A Compare with
17424 None - 21 0 Manual N/A Compare with
566 None - 12 0 Manual* N/A Compare with
17217 None - 31 1 Manual N/A Compare with
17515 None - 26 0 Manual N/A Compare with
2671 None - 47 -3 Manual N/A Compare with
17309 None - 25 -1 Manual N/A Compare with
17547 None - 26 1 Manual N/A Compare with
17161 None - 23 0 Manual N/A Compare with
4578 None - 161 -8 Manual* N/A Compare with
17400 None - 21 0 Manual N/A Compare with
171 None - 14 0 Manual* N/A Compare with
17193 None - 28 0 Manual N/A Compare with
17432 None - 15 0 Manual N/A Compare with
574 None - 17 0 Manual* N/A Compare with
1649 None - 5 0 Manual* N/A Compare with
17284 None - 23 0 Manual N/A Compare with
17523 None - 21 -1 Manual N/A Compare with
2920 None - 27 1 Manual N/A Compare with
17317 None - 24 0 Manual N/A Compare with
18621 None - 49 -3 Manual* N/A Compare with
17169 None - 28 0 Manual N/A Compare with
17408 None - 28 -1 Manual N/A Compare with
203 None - 22 0 Manual* N/A Compare with
9377 None - 12 -2 Manual* N/A Compare with
17381 None - 23 0 Manual N/A Compare with
17233 None - 26 0 Manual N/A Compare with
17472 None - 24 0 Manual N/A Compare with
1564 None - 143 0 Manual* N/A Compare with
17265 None - 19 0 Manual N/A Compare with
17504 None - 32 0 Manual N/A Compare with
5182 None - 110 -8 Manual* N/A Compare with
1606 None - 20 0 Manual* N/A Compare with
17357 None - 30 0 Manual N/A Compare with
17150 None - 16 -1 Manual N/A Compare with
17389 None - 18 0 Manual N/A Compare with
17241 None - 26 -1 Manual N/A Compare with
17480 None - 27 -1 Manual N/A Compare with
1576 None - 129 0 Manual* N/A Compare with
17273 None - 24 -1 Manual N/A Compare with
5814 None - 381 1 Manual* N/A Compare with
17365 None - 29 0 Manual N/A Compare with
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ATB Pipeline Setting

Access to this feature is currently restricted

The maximum QM level is computed using the ATB Pipeline atom limits but can be manually increased on a case by case basis.

Experimental Solvation Free Energies (0-0 of 0)